Advice needed. Sanity not required.

First allow me thank all who comment in advance for advice on the proposed problem in which I now find myself, and apologise as well for the inevitable narrative below.

I graduated (in 4 years) with a B.S. Physics from UCSB in '04 with a so-so physics gpa (~3.3) and a heavy course load of math (I believe I was only one or two classes from a double major but had hit a credit cap) . My electives were mostly concentrated in quantum, QCD/particle and QED with a graduate class in QM as well. I, of course, did participate in senior lab for a full two semesters in preparation for graduate school. Also, because I love research, I volunteered time as an undergrad in an astrophysics lab.

As a typical "prospective" grad student at the time I took the GRE and PGRE. All was fairly well... Now boost the reference frame to today and my current dilemma.

After I graduated I decided not to go to graduate school right away but to work because I have seen first hand the difficulties of soft money research (My father is a microbiology professor at the Salk Institute in San Diego, CA). I spent some time after graduation working in microbiology but later moved across country and ended up in a different field entirely (namely computer engineering). Long story short I excelled in that field and now work for the Department of Defense building future terminators and advancing SKYNET ;) (true story btw)

I have been struggling over the past year (perhaps two) with the decisions I have made in my life and have decided that I will never find personal satisfaction unless I return to school so I can pursue my interests in HEP research (CMS/ATLAS and the like). In one way, I suppose, I am glad I made the decision to initially delay grad school I believe the delay has matured me to a point where I am now ready to fully appreciate the level of commitment and dedicate myself entirely to the pursuit of the degree - in short I am serious about my passion now.

None-the-less I now find myself having a number of obstacles which need to be overcome and was hoping that some of you may enlighten me as to possible solutions. I am already aware of the expiration dates of GRE/PGRE and am going to retake before reapplication this year. I have already begun (some time ago) revisiting my undergraduate work as to not forget key concepts and problems for qualifying exams. However, my three largest obstacles still remain (due to time passage):

1) No current research background to talk about in personal statement
2) No letters from academic/physics professors
3) I am not allowed to discuss much about my current job

Has anyone encountered any of these issues? If so how did you tackle them in a way that did not dwell but still effectively conveyed your passion for physics?

My father sits on the board for graduate admissions at UCSD (for molecular biology) and while I highly value his opinion he is, at the end of the day, not a physicist.

My only hopes, as I see it are:
1) my GPA is not good, but not horrible
2) the school I went to was pretty tough for physics and most physics grad depts have heard of it
3) I am not married/no children so that would not appear as an impediment to study
4) I would now be leaving a high paying, stable job in order to pursue this degree which I believe shows my commitment/seriousness in finishing.

With respect to research experience, stuff that you did six years ago can still count. Admissions committees aren't usually interested in what you've done, so much as the experience you've collected along the way. In that respect, working out in the real world for a while may actually give you a little bit of a leg up over other prospective students.

Depending on the requirements, if you don't have professors to ask for references, you can speak to your current supervisor. He or she will be in a position to provide a reference and that will also solve the issue of what you can and cannot talk about outside of work. Another way around this is to start doing some volunteer work at a local college or university. It might also be worth contacting some of your previous professors. Explain your situation and they might remember something about you.

A final thing to consider is that if you've been working for a few years, you may qualify as a "mature student" and the applicaton process may be slightly different. Make sure you look into this with the schools you're interested in.

@OP, you're in a pretty nice position right now. The DOD has identified a lack of "geeks" as a national security issue, and they may work hard to make you happy for the purpose of retaining you. Do you see opportunities branching from your current position that might be more satisfying to you? If so, you might want to express an interest in pursuing those and mention that you are considering going to grad school. If you've been doing a good job, you'll probably be short-listed for transfer/promotion.

That's definitely the case at the DoD right now. However certain positions are graded based on educational qualifications. Be it experimental soft money research or govt research at the end of the day I'm not really worried about getting a job after completion, I'm more worried about getting into graduate school in the first place.

As far as staying govt, I'd rather sacrifice the pay and security for the possibility to get my degree and research in the area of my interests.

If you're suggesting a xfer to another department for experience, I can see the added benefit of that and considered it. However I don't think it would justify delaying my PhD even farther and I doubt a grad committee will either.
:)